Online_DPI: a web server to calculate the diffraction precision index for a protein structure

An online computing server, Online_DPI (where DPI denotes the diffraction precision index), has been created to calculate the `Cruickshank DPI' value for a given three-dimensional protein or macromolecular structure. It also estimates the atomic coordinate error for all the atoms available in the structure. It is an easy-to-use web server that enables users to visualize the computed values dynamically on the client machine. Users can provide the Protein Data Bank (PDB) identification code or upload the three-dimensional atomic coordinates from the client machine. The computed DPI value for the structure and the atomic coordinate errors for all the atoms are included in the revised PDB file. Further, users can graphically view the atomic coordinate error along with `temperature factors' (i.e. atomic displacement parameters). In addition, the computing engine is interfaced with an up-to-date local copy of the Protein Data Bank. New entries are updated every week, and thus users can access all the structures available in the Protein Data Bank. The computing engine is freely accessible online at http://cluster.physics.iisc.ernet.in/dpi/.

Influence of external weld flash on the in-plane plane-strain formability of friction stir welded sheets

The main aim of the present work is to analyze the influence of external weld flash on the formability of friction stir welding sheets through in-plane plane-strain formability tests. The load-extension behavior and forming limit strains are measured to quantify the formability. The influence of friction stir welding parameters on the height of weld flash was also studied. The base materials used for welding trials are AA6061T6 and AA5052H32 alloy sheets of 2.1-mm thickness. It is observed that the influence of external weld flash on the maximum load and total extension for all the friction stir welding conditions is negligible. The effect of weld flash on the limiting major strain is also insignificant. But the presence of weld flash has changed the limiting minor strain, more toward plane-strain condition, indicating the change in strain-path toward plane-strain. This is due to the strain taken by weld flash, along with the major strain, minor strain, and thickness strain in the friction stir welding sheet plane because of constancy of volume. The formation of weld flash and its height are affected synergistically by the axial force and temperature development during friction stir welding. The higher the axial force and temperature, the higher the flash height.

A Variant of the Hadwiger-Debrunner (p, q)-Problem in the Plane

Let X be a convex curve in the plane (say, the unit circle), and let be a family of planar convex bodies such that every two of them meet at a point of X. Then has a transversal of size at most . Suppose instead that only satisfies the following ``(p, 2)-condition'': Among every p elements of , there are two that meet at a common point of X. Then has a transversal of size . For comparison, the best known bound for the Hadwiger-Debrunner (p, q)-problem in the plane, with , is . Our result generalizes appropriately for if is, for example, the moment curve.

Mono layer to Interdigitated Partial Bilayer Smectic C Transition in Thiophene-Based Spacer Mesogens: X-ray Diffraction and C-13 Nuclear Magnetic Resonance Studies

Mesophase organization of molecules built with thiophene at the center and linked via flexible spacers to rigid side arm core units and terminal alkoxy chains has been investigated. Thirty homologues realized by varying the span of the spacers as well as the length of the terminal chains have been studied. In addition to the enantiotropic nematic phase observed for all the mesogens, the increase of the spacer as well as the terminal chain lengths resulted in the smectic C phase. The molecular organization in the smectic phase as investigated by temperature dependent X-ray diffraction measurements revealed an interesting behavior that depended on the length of the spacer vis-a-vis the length of the terminal chain. Thus, a tilted interdigitated partial bilayer organization was observed for molecules with a shorter spacer length, while a tilted monolayer arrangement was observed for those with a longer spacer length. High-resolution solid state C-13 NMR studies carried out for representative mesogens indicated a U-shape for all the molecules, indicating that intermolecular interactions and molecular dynamics rather than molecular shape are responsible for the observed behavior. Models for the mesophase organization have been considered and the results understood in terms of segregation of incompatible parts of the mesogens combined with steric frustration leading to the observed lamellar order.

In-plane elastic responses of circular cell honeycombs and bundled circular tubes in a diamond array structure

Assemblages of circular tubes and circular honeycombs in close packed arrangement are presently both competing and complementing regular honeycomb structures (HCS). The intrinsic isotropy of bundled tubes/rings in hexagonal arrays restricts their use to applications with isotopic need. With the aim of extending the utility of tubes/rings assemblages to anisotropic needs, this paper explores the prospects of bundled tubes and circular honeycombs in a general diamond array structure (DAS) to cater these needs. To this end, effective transverse Young's moduli and Poisson's ratio for thick/thin DAS are obtained theoretically. Analysis frameworks including thin ring theory (TRT), curved beam theory (CBT) and elasticity formulations are tested and corroborated by FEA employing contact elements. Results indicate that TRT and CBT are reasonable for thin tubes and honeycombs. Nevertheless, TRT yields compact formulae to study the anisotropy ratio, moduli spectrum and sensitivity of the assemblage as a function of thicknesses and array structure. These formulae supplement designers as a guide to tailor the structures. On the other hand, elasticity formulation can estimate over a larger range including very thick tubes/rings. In addition, this formulation offers to estimate refined transverse strengths of assemblages. (C) 2015 Elsevier Ltd. All rights reserved.

In-plane effective shear modulus of generalized circular honeycomb structures and bundled tubes in a diamond array structure

Use of circular hexagonal honeycomb structures and tube assemblies in energy absorption systems has attracted a large number of literature on their characterization under crushing and impact loads. Notwithstanding these, effective shear moduli (G*) required for complete transverse elastic characterization and in analyses of hierarchical structures have received scant attention. In an attempt to fill this void, the present study undertakes to evaluate G* of a generalized circular honeycomb structures and tube assemblies in a diamond array structure (DAS) with no restriction on their thickness. These structures present a potential to realize a spectrum of moduli with minimal modifications, a point of relevance for manufactures and designers. To evaluate G* in this paper, models based on technical theories - thin ring theory and curved beam theory - and rigorous theory of elasticity are investigated and corroborated with FEA employing contact elements. Technical theories which give a good match for thin HCS offer compact expressions for moduli which can be harvested to study sensitivity of moduli on topology. On the other hand, elasticity model offers a very good match over a large range of thickness along with exact analysis of stresses by employing computationally efficient expressions. (C) 2015 Elsevier Ltd. All rights reserved.

Transport properties of solution processed Cu2SnS3/AZnO heterostructure for low cost photovoltaics

Cu2SnS3 thin films were deposited by a facile sot-gel technique followed by annealing. The annealed films were structurally characterized by grazing incidence X-ray diffraction (GIXRD) and transmission electron microscopy (TEM). The crystal structure was found to be tetragonal with crystallite sizes of 2.4-3 nm. Texture coefficient calculations from the GIXRD revealed the preferential orientation of the film along the (112) plane. The morphological investigations of the films were carried out using field emission scanning electron microscopy (FESEM) and the composition using electron dispersive spectroscopy (EDS). The temperature dependent current, voltage characteristics of the Cu2SnS3/AZnO heterostructure were studied. The log I-log V plot exhibited three regions of different slopes showing linear ohmic behavior and non-linear behavior following the power law. The temperature dependent current voltage characteristics revealed the variation in ideality factor and barrier height with temperature. The Richardson constant was calculated and its deviation from the theoretical value revealed the inhomogeneity of the barrier heights. Transport characteristics were modeled using the thermionic emission model. The Gaussian distribution of barrier heights was applied and from the modified Richardson plot the value of the Richardson constant was found to be 47.18 A cm(-2) K-2. (c) 2015 Elsevier B.V. All rights reserved.

Onset of plane layer magnetoconvection at low Ekman number

We study the onset of magnetoconvection between two infinite horizontal planes subject to a vertical magnetic field aligned with background rotation. In order to gain insight into the convection taking place in the Earth's tangent cylinder, we target regimes of asymptotically strong rotation. The critical Rayleigh number Ra-c and critical wavenumber a(c) are computed numerically by solving the linear stability problem in a systematic way, with either stress-free or no-slip kinematic boundary conditions. A parametric study is conducted, varying the Ekman number E (ratio of viscous to Coriolis forces) and the Elsasser number. (ratio of the Lorentz force to the Coriolis force). E is varied from 10(-9) to 10(-2) and. from 10(-3) to 1. For a wide range of thermal and magnetic Prandtl numbers, our results verify and confirm previous experimental and theoretical results showing the existence of two distinct unstable modes at low values of E-one being controlled by the magnetic field, the other being controlled by viscosity (often called the viscous mode). It is shown that oscillatory onset does not occur in the range of parameters we are interested in. Asymptotic scalings for the onset of these modes are numerically confirmed and their domain of validity is precisely quantified. We show that with no-slip boundary conditions, the asymptotic behavior is reached for E < 10(-6) and establish a map in the (E, Lambda) plane. We distinguish regions where convection sets in either through the magnetic mode or through the viscous mode. Our analysis gives the regime in which the transition between magnetic and viscous modes may be observed. We also show that within the asymptotic regime, the role played by the kinematic boundary conditions is minimal. (C) 2015 AIP Publishing LLC.

Structural and optical characterization of nonpolar (10-10) m-InN/m-GaN epilayers grown by PAMBE

Plasma-assisted molecular beam epitaxy growth of (10-10) m-InN/(10-10) m-GaN was carried out on bare (10-10) m-sapphire substrate. The high resolution X-ray diffraction studies confirmed the orientation of the as-grown films. Nonpolar InN layer was grown at different growth temperatures ranging from 390 degrees C to 440 degrees C and the FWHM of rocking curve revealed good quality film at low temperatures. An in-plane relationship was established for the hetrostructures using phi-scan and a perfect alignment was found for the epilayers. Change of morphology of the films grown at different temperatures was observed using an atomic force microscopy technique showing the smoothest film grown at 400 degrees C. InN optical band gap was found to be vary from 0.79-0.83 eV from absorption spectra. The blue-shift of absorption edge was found to be induced by excess background electron concentration. (C) 2015 Elsevier B.V. All rights reserved.

Neutron powder diffraction study of Ba3ZnRu2-xIrxO9 (x=0, 1, 2) with 6H-type perovskite structure

The triple perovskites Ba3ZnRu2-xIrxO9 with x = 0, 1, and 2 are insulating compounds in which Ru(Ir) cations form a dimer state. Polycrystalline samples of these materials were studied using neutron powder diffraction (NPD) at 10 and 295 K. No structural transition nor evidence of long range magnetic order was observed within the investigated temperature range. The results from structural refinements of the NPD data and its polyhedral analysis are presented, and discussed as a function of Ru/Ir content. (C) 2015 Elsevier Masson SAS. All rights reserved.

Neutron diffraction, Mossbauer effect and Electron Paramagnetic Resonance studies on multiferroic Pb(Fe2/3W1/3)O-3

Multiferroic Pb(Fe2/3W1/3)O-3 ceramics were synthesized via a modified two-stage Columbite method. Single phase formation was confirmed from the analysis of x-ray and neutron diffraction patterns recorded at room temperature. Structural analysis of the diffraction data reveals cubic phase (space group Pm-3m) for the title compound. Magnetic structure of the title compound at room temperature exhibits G-type antiferromagnetic structure. The Mossbauer spectroscopy and Electron Paramagnetic Resonance (EPR) studies were carried out at 300 K. The isomer shift and quadrupole splitting of the Mossbauer spectra confirms the trivalent state of iron (Fe3+). The Mossbauer spectra also suggest that the iron and tungsten are randomly distributed at the octahedral, B site. EPR spectra show a single broad line associated with Fe3+ ions. Both spectra clearly exhibit weak ferromagnetic behaviour of Pb(Fe2/3W1/3)O-3 ceramic at 300 K. Considering neutron diffraction, Mossbauer and EPR results together, it may be stated here that Pb(Fe2/3W1/3)O-3 exhibits antiferromagnetic behavior along with weak ferromagnetism at room temperature.

Efficient coupled polynomial interpolation scheme for out-of-plane free vibration analysis of curved beams

The performance of two curved beam finite element models based on coupled polynomial displacement fields is investigated for out-of-plane vibration of arches. These two-noded beam models employ curvilinear strain definitions and have three degrees of freedom per node namely, out-of-plane translation (v), out-of-plane bending rotation (theta(z)) and torsion rotation (theta(s)). The coupled polynomial interpolation fields are derived independently for Timoshenko and Euler-Bernoulli beam elements using the force-moment equilibrium equations. Numerical performance of these elements for constrained and unconstrained arches is compared with the conventional curved beam models which are based on independent polynomial fields. The formulation is shown to be free from any spurious constraints in the limit of `flexureless torsion' and `torsionless flexure' and hence devoid of flexure and torsion locking. The resulting stiffness and consistent mass matrices generated from the coupled displacement models show excellent convergence of natural frequencies in locking regimes. The accuracy of the shear flexibility added to the elements is also demonstrated. The coupled polynomial models are shown to perform consistently over a wide range of flexure-to-shear (EI/GA) and flexure-to-torsion (EI/GJ) stiffness ratios and are inherently devoid of flexure, torsion and shear locking phenomena. (C) 2015 Elsevier B.V. All rights reserved.

Determinantal point processes in the plane from products of random matrices

We show that the density of eigenvalues for three classes of random matrix ensembles is determinantal. First we derive the density of eigenvalues of product of k independent n x n matrices with i.i.d. complex Gaussian entries with a few of matrices being inverted. In second example we calculate the same for (compatible) product of rectangular matrices with i.i.d. Gaussian entries and in last example we calculate for product of independent truncated unitary random matrices. We derive exact expressions for limiting expected empirical spectral distributions of above mentioned ensembles.

Clean localization super-resolution microscopy for 3D biological imaging

We propose clean localization microscopy (a variant of fPALM) using a molecule filtering technique. Localization imaging involves acquiring a large number of images containing single molecule signatures followed by one-to-one mapping to render a super-resolution image. In principle, this process can be repeated for other z-planes to construct a 3D image. But, single molecules observed from off-focal planes result in false representation of their presence in the focal plane, resulting in incorrect quantification and analysis. We overcome this with a single molecule filtering technique that imposes constraints on the diffraction limited spot size of single molecules in the image plane. Calibration with sub-diffraction size beads puts a natural cutoff on the actual diffraction-limited size of single molecules in the focal plane. This helps in distinguishing beads present in the focal plane from those in the off-focal planes thereby providing an estimate of the single molecules in the focal plane. We study the distribution of actin (labeled with a photoactivatable CAGE 552 dye) in NIH 3T3 mouse fibroblast cells. (C) 2016 Author(s).

Magnetic structures and magnetic phase transitions in the Mn-doped orthoferrite TbFeO3 studied by neutron powder diffraction

The magnetic structures and the magnetic phase transitions in the Mn-doped orthoferrite TbFeO3 studied using neutron powder diffraction are reported. Magnetic phase transitions are identified at T-N(Fe/Mn) approximate to 295K where a paramagnetic-to-antiferromagnetic transition occurs in the Fe/Mn sublattice, T-SR(Fe/Mn) approximate to 26K where a spin-reorientation transition occurs in the Fe/Mn sublattice and T-N(R) approximate to 2K where Tb-ordering starts to manifest. At 295 K, the magnetic structure of the Fe/Mn sublattice in TbFe0.5Mn0.5O3 belongs to the irreducible representation Gamma(4) (G(x)A(y)F(z) or Pb'n'm). A mixed-domain structure of (Gamma(1) + Gamma(4)) is found at 250K which remains stable down to the spin re-orientation transition at T-SR(Fe/Mn) approximate to 26K. Below 26K and above 250 K, the majority phase (>80%) is that of Gamma(4). Below 10K the high-temperature phase Gamma(4) remains stable till 2K. At 2 K, Tb develops a magnetic moment value of 0.6(2) mu(B)/f.u. and orders long-range in F-z compatible with the Gamma(4) representation. Our study confirms the magnetic phase transitions reported already in a single crystal of TbFe0.5Mn0.5O3 and, in addition, reveals the presence of mixed magnetic domains. The ratio of these magnetic domains as a function of temperature is estimated from Rietveld refinement of neutron diffraction data. Indications of short-range magnetic correlations are present in the low-Q region of the neutron diffraction patterns at T < T-SR(Fe/Mn). These results should motivate further experimental work devoted to measure electric polarization and magnetocapacitance of TbFe0.5Mn0.5O3. (C) 2016 AIP Publishing LLC.